Learning to do multiframe wavefront sensing unsupervisedly: applications to blind deconvolution

Observations from ground based telescopes are affected by the presence of the Earth atmosphere, which severely perturbs them. The use of adaptive optics techniques has allowed us to partly beat this limitation. However, image selection or post-facto image reconstruction methods applied to bursts of short-exposure images are routinely needed to reach the diffraction limit. Deep learning has been recently proposed as an efficient way to accelerate these image reconstructions. Currently, these deep neural networks are trained with supervision, so that either standard deconvolution algorithms need to be applied a-priori or complex simulations of the solar magneto-convection need to be carried out to generate the training sets. Our aim here is to propose a general unsupervised training scheme that allows multiframe blind deconvolution deep learning systems to be trained simply with observations. The approach can be applied for the correction of point-like as well as extended objects. Leveraging the linear image formation theory and a probabilistic approach to the blind deconvolution problem produces a physically-motivated loss function. The optimization of this loss function allows an end-to-end training of a machine learning model composed of three neural networks. As examples, we apply this procedure to the deconvolution of stellar data from the FastCam instrument and to solar extended data from the Swedish Solar Telescope. The analysis demonstrates that the proposed neural model can be successfully trained without supervision using observations only. It provides estimations of the instantaneous wavefronts, from which a corrected image can be found using standard deconvolution technniques. The network model is roughly three orders of magnitude faster than applying standard deconvolution based on optimization and shows potential to be used on real-time at the telescope.Comment: 11 pages, 4 figures, accepted for publication in A&

Towards the automatic estimation of gravitational lenses' time delays

Estimation of time delays from a noisy and gapped data is one of the simplest data analysis problems in astronomy by its formulation. But as history of real experiments show, the work with observed data sets can be quite complex and evolved. By analysing in detail previous attempts to build delay estimation algorithms we try to develop an automatic and robust procedure to perform the task. To evaluate and compare different variants of the algorithms we use real observed data sets which have been objects of past controversies. In this way we hope to select the methods and procedures which have highest probability to succeed in complex situations. As a result of our investigations we propose an estimation procedure which can be used as a method of choice in large photometric experiments. We can not claim that proposed methodology works with any reasonably well sampled input data set. But we hope that the steps taken are in correct direction and developed software is truly useful for practising astronomers.Comment: Accepted by Baltic Astronomy, 21 pages, 4 figure

Protein-RNA linkage and post-translational modifications of two sobemovirus VPgs

Sobemoviruses possess a viral genome-linked protein (VPg) attached to the 5' end of viral RNA. VPg is processed from the viral polyprotein. In the current study, Cocksfoot mottle virus (CfMV) and Rice yellow mottle virus (RYMV) VPgs were purified from virions and analysed by mass spectrometry. The cleavage sites in the polyprotein and thereof the termini of VPg were experimentally proven. The lengths of the mature VPgs were determined to be 78 and 79 aa residues, respectively. The amino acid residues covalently linked to RNA in the two VPgs were, surprisingly, not conserved; it is a tyrosine at position 5 of CfMV VPg and serine at position 1 of RYMV VPg. Phosphorylations were identified in CfMV and RYMV VPgs with two positionally similar locations T20/S14 and S71/S72, respectively. RYMV VPg contains an additional phosphorylation site at S41

Sobemovirus RNA linked to VPg over a threonine residue

AbstractPositive sense ssRNA virus genomes from several genera have a viral protein genome-linked (VPg) attached over a phosphodiester bond to the 5′ end of the genome. The VPgs of Southern bean mosaic virus (SBMV) and Ryegrass mottle virus (RGMoV) were purified from virions and analyzed by mass spectrometry. SBMV VPg was determined to be linked to RNA through a threonine residue at position one, whereas RGMoV VPg was linked to RNA through a serine also at the first position. In addition, we identified the termini of the corresponding VPgs and discovered three and seven phosphorylation sites in SBMV and RGMoV VPgs, respectively. This is the first report on the use of threonine for linking RNA to VPg

Solar-Cycle Variation of quiet-Sun Magnetism and Surface Gravity Oscillation Mode

The origin of the quiet Sun magnetism is under debate. Investigating the solar cycle variation observationally in more detail can give us clues about how to resolve the controversies. We investigate the solar cycle variation of the most magnetically quiet regions and their surface gravity oscillation ($f$-) mode integrated energy ($E_f$). We use 12 years of HMI data and apply a stringent selection criteria, based on spatial and temporal quietness, to avoid any influence of active regions (ARs). We develop an automated high-throughput pipeline to go through all available magnetogram data and to compute $E_f$ for the selected quiet regions. We observe a clear solar cycle dependence of the magnetic field strength in the most quiet regions containing several supergranular cells. For patch sizes smaller than a supergranular cell, no significant cycle dependence is detected. The $E_f$ at the supergranular scale is not constant over time. During the late ascending phase of Cycle 24 (SC24, 2011-2012), it is roughly constant, but starts diminishing in 2013, as the maximum of SC24 is approached. This trend continues until mid-2017, when hints of strengthening at higher southern latitudes are seen. Slow strengthening continues, stronger at higher latitudes than at the equatorial regions, but $E_f$ never returns back to the values seen in 2011-2012. Also, the strengthening trend continues past the solar minimum, to the years when SC25 is already clearly ascending. Hence the $E_f$ behavior is not in phase with the solar cycle. The anticorrelation of $E_f$ with the solar cycle in gross terms is expected, but the phase shift of several years indicates a connection to the poloidal large-scale magnetic field component rather than the toroidal one. Calibrating AR signals with the QS $E_f$ does not reveal significant enhancement of the $f$-mode prior to AR emergence.Comment: 10 pages, 11 figures, submitted to Astronomy & Astrophysic

Protein-RNA linkage and posttranslational modifications of feline calicivirus and murine norovirus VPg proteins.

Members of the Caliciviridae family of positive sense RNA viruses cause a wide range of diseases in both humans and animals. The detailed characterization of the calicivirus life cycle had been hampered due to the lack of robust cell culture systems and experimental tools for many of the members of the family. However, a number of caliciviruses replicate efficiently in cell culture and have robust reverse genetics systems available, most notably feline calicivirus (FCV) and murine norovirus (MNV). These are therefore widely used as representative members with which to examine the mechanistic details of calicivirus genome translation and replication. The replication of the calicivirus RNA genome occurs via a double-stranded RNA intermediate that is then used as a template for the production of new positive sense viral RNA, which is covalently linked to the virus-encoded protein VPg. The covalent linkage to VPg occurs during genome replication via the nucleotidylylation activity of the viral RNA-dependent RNA polymerase. Using FCV and MNV, we used mass spectrometry-based approach to identify the specific amino acid linked to the 5' end of the viral nucleic acid. We observed that both VPg proteins are covalently linked to guanosine diphosphate (GDP) moieties via tyrosine positions 24 and 26 for FCV and MNV respectively. These data fit with previous observations indicating that mutations introduced into these specific amino acids are deleterious for viral replication and fail to produce infectious virus. In addition, we also detected serine phosphorylation sites within the FCV VPg protein with positions 80 and 107 found consistently phosphorylated on VPg-linked viral RNA isolated from infected cells. This work provides the first direct experimental characterization of the linkage of infectious calicivirus viral RNA to the VPg protein and highlights that post-translational modifications of VPg may also occur during the viral life cycle.Funding is provided by Wellcome Trust (Ref: 097997/Z/11/Z) and the institutional research funding IUT19-3 from the Estonian Ministry of Education and Research.This is the final version of the article. It first appeared from PeerJ via https://doi.org/10.7717/peerj.213

Shapes of stellar activity cycles

Context.Magnetic activity cycles are an important phenomenon both in the Sun and other stars. The shape of the solar cycle is commonly characterised by a fast rise and a slower decline, but not much attention has been paid to the shape of cycles in other stars. Aims.Our aim is to study whether the asymmetric shape of the solar cycle is common in other stars as well, and compare the cycle asymmetry to other stellar parameters. We also study the differences in the shape of the solar cycle, depending on the activity indicator that is used. The observations are also compared to simulated activity cycles. Methods.We used the chromospheric Ca II H&K data from the Mount Wilson Observatory HK Project. In this data set, we identified 47 individual cycles from 18 stars. We used the statistical skewness of a cycle as a measure of its asymmetry, and compared this to other stellar parameters. A similar analysis has been performed for magnetic cycles extracted from direct numerical magnetohydrodynamic simulations of solar-type convection zones. Results.The shape of the solar cycle (fast rise and slower decline) is common in other stars as well, although the Sun seems to have particularly asymmetric cycles. Cycle-to-cycle variations are large, but the average shape of a cycle is still fairly well represented by a sinusoid, although this does not take its asymmetry into account. We find only slight correlations between the cycle asymmetry and other stellar parameters. There are large differences in the shape of the solar cycle, depending on the activity indicator that is used. The simulated cycles differ in the symmetry of global simulations that cover the full longitudinal range and are therefore capable of exciting non-axisymmetric large-scale dynamo modes, and wedge simulations that cover a partial extent in longitude, where only axisymmetric large-scale modes are possible. The former preferentially produce positive and the latter negative skewness.Peer reviewe

Transcriptional slippage in the positive-sense RNA virus family Potyviridae.

The family Potyviridae encompasses ~30% of plant viruses and is responsible for significant economic losses worldwide. Recently, a small overlapping coding sequence, termed pipo, was found to be conserved in the genomes of all potyvirids. PIPO is expressed as part of a frameshift protein, P3N-PIPO, which is essential for virus cell-to-cell movement. However, the frameshift expression mechanism has hitherto remained unknown. Here, we demonstrate that transcriptional slippage, specific to the viral RNA polymerase, results in a population of transcripts with an additional "A" inserted within a highly conserved GAAAAAA sequence, thus enabling expression of P3N-PIPO. The slippage efficiency is ~2% in Turnip mosaic virus and slippage is inhibited by mutations in the GAAAAAA sequence. While utilization of transcriptional slippage is well known in negative-sense RNA viruses such as Ebola, mumps and measles, to our knowledge this is the first report of its widespread utilization for gene expression in positive-sense RNA viruses.Work in the AEF laboratory was funded by grants from the WellcomeTrust [088789], [106207] and Biotechnology and Biological ResearchCouncil (BBSRC) [BB/J007072/1], [BB/J015652/1]. Work in the JPC laboratorywas funded by BBSRC grants [BB/J015652/1], [BB/J011762/1]. BYWC wassupported by a Sir Henry Wellcome Postdoctoral Fellowship [096082]and an EMBL long-term postdoctoral fellowship

Multiperiodicity, modulations and flip-flops in variable star light curves I. Carrier fit method

The light curves of variable stars are commonly described using simple trigonometric models, that make use of the assumption that the model parameters are constant in time. This assumption, however, is often violated, and consequently, time series models with components that vary slowly in time are of great interest. In this paper we introduce a class of data analysis and visualization methods which can be applied in many different contexts of variable star research, for example spotted stars, variables showing the Blazhko effect, and the spin-down of rapid rotators. The methods proposed are of explorative type, and can be of significant aid when performing a more thorough data analysis and interpretation with a more conventional method.Our methods are based on a straightforward decomposition of the input time series into a fast "clocking" periodicity and smooth modulating curves. The fast frequency, referred to as the carrier frequency, can be obtained from earlier observations (for instance in the case of photometric data the period can be obtained from independently measured radial velocities), postulated using some simple physical principles (Keplerian rotation laws in accretion disks), or estimated from the data as a certain mean frequency. The smooth modulating curves are described by trigonometric polynomials or splines. The data approximation procedures are based on standard computational packages implementing simple or constrained least-squares fit-type algorithms.Comment: 14 pages, 23 figures, submitted to Astronomy and Astrophysic